Job ID = 6455314 SRX = SRX287688 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:56:56 prefetch.2.10.7: 1) Downloading 'SRR869876'... 2020-06-21T09:56:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:00:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:00:09 prefetch.2.10.7: 1) 'SRR869876' was downloaded successfully Read 21539662 spots for SRR869876/SRR869876.sra Written 21539662 spots for SRR869876/SRR869876.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:05 21539662 reads; of these: 21539662 (100.00%) were unpaired; of these: 1287674 (5.98%) aligned 0 times 13644138 (63.34%) aligned exactly 1 time 6607850 (30.68%) aligned >1 times 94.02% overall alignment rate Time searching: 00:06:05 Overall time: 00:06:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2680984 / 20251988 = 0.1324 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:12:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:12:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:56: 1000000 INFO @ Sun, 21 Jun 2020 19:13:02: 2000000 INFO @ Sun, 21 Jun 2020 19:13:08: 3000000 INFO @ Sun, 21 Jun 2020 19:13:13: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:13:19: 5000000 INFO @ Sun, 21 Jun 2020 19:13:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:13:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:26: 6000000 INFO @ Sun, 21 Jun 2020 19:13:26: 1000000 INFO @ Sun, 21 Jun 2020 19:13:32: 7000000 INFO @ Sun, 21 Jun 2020 19:13:33: 2000000 INFO @ Sun, 21 Jun 2020 19:13:38: 8000000 INFO @ Sun, 21 Jun 2020 19:13:39: 3000000 INFO @ Sun, 21 Jun 2020 19:13:45: 9000000 INFO @ Sun, 21 Jun 2020 19:13:45: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:13:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:51: 10000000 INFO @ Sun, 21 Jun 2020 19:13:52: 5000000 INFO @ Sun, 21 Jun 2020 19:13:56: 1000000 INFO @ Sun, 21 Jun 2020 19:13:58: 11000000 INFO @ Sun, 21 Jun 2020 19:13:59: 6000000 INFO @ Sun, 21 Jun 2020 19:14:03: 2000000 INFO @ Sun, 21 Jun 2020 19:14:05: 12000000 INFO @ Sun, 21 Jun 2020 19:14:05: 7000000 INFO @ Sun, 21 Jun 2020 19:14:09: 3000000 INFO @ Sun, 21 Jun 2020 19:14:11: 13000000 INFO @ Sun, 21 Jun 2020 19:14:12: 8000000 INFO @ Sun, 21 Jun 2020 19:14:16: 4000000 INFO @ Sun, 21 Jun 2020 19:14:18: 14000000 INFO @ Sun, 21 Jun 2020 19:14:18: 9000000 INFO @ Sun, 21 Jun 2020 19:14:22: 5000000 INFO @ Sun, 21 Jun 2020 19:14:25: 15000000 INFO @ Sun, 21 Jun 2020 19:14:25: 10000000 INFO @ Sun, 21 Jun 2020 19:14:29: 6000000 INFO @ Sun, 21 Jun 2020 19:14:32: 16000000 INFO @ Sun, 21 Jun 2020 19:14:32: 11000000 INFO @ Sun, 21 Jun 2020 19:14:36: 7000000 INFO @ Sun, 21 Jun 2020 19:14:38: 17000000 INFO @ Sun, 21 Jun 2020 19:14:39: 12000000 INFO @ Sun, 21 Jun 2020 19:14:42: 8000000 INFO @ Sun, 21 Jun 2020 19:14:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:43: #1 total tags in treatment: 17571004 INFO @ Sun, 21 Jun 2020 19:14:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:14:43: #1 tags after filtering in treatment: 17571004 INFO @ Sun, 21 Jun 2020 19:14:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:44: #2 number of paired peaks: 419 WARNING @ Sun, 21 Jun 2020 19:14:44: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:44: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 19:14:44: #2 alternative fragment length(s) may be 4,100,117 bps INFO @ Sun, 21 Jun 2020 19:14:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.05_model.r WARNING @ Sun, 21 Jun 2020 19:14:44: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:14:44: #2 You may need to consider one of the other alternative d(s): 4,100,117 WARNING @ Sun, 21 Jun 2020 19:14:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:14:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:46: 13000000 INFO @ Sun, 21 Jun 2020 19:14:49: 9000000 INFO @ Sun, 21 Jun 2020 19:14:53: 14000000 INFO @ Sun, 21 Jun 2020 19:14:56: 10000000 INFO @ Sun, 21 Jun 2020 19:15:00: 15000000 INFO @ Sun, 21 Jun 2020 19:15:03: 11000000 INFO @ Sun, 21 Jun 2020 19:15:07: 16000000 INFO @ Sun, 21 Jun 2020 19:15:10: 12000000 INFO @ Sun, 21 Jun 2020 19:15:14: 17000000 INFO @ Sun, 21 Jun 2020 19:15:17: 13000000 INFO @ Sun, 21 Jun 2020 19:15:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:18: #1 total tags in treatment: 17571004 INFO @ Sun, 21 Jun 2020 19:15:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:15:18: #1 tags after filtering in treatment: 17571004 INFO @ Sun, 21 Jun 2020 19:15:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:20: #2 number of paired peaks: 419 WARNING @ Sun, 21 Jun 2020 19:15:20: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:20: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 19:15:20: #2 alternative fragment length(s) may be 4,100,117 bps INFO @ Sun, 21 Jun 2020 19:15:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.10_model.r WARNING @ Sun, 21 Jun 2020 19:15:20: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:20: #2 You may need to consider one of the other alternative d(s): 4,100,117 WARNING @ Sun, 21 Jun 2020 19:15:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:15:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:20: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:15:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:24: 14000000 INFO @ Sun, 21 Jun 2020 19:15:31: 15000000 INFO @ Sun, 21 Jun 2020 19:15:37: 16000000 INFO @ Sun, 21 Jun 2020 19:15:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.05_summits.bed INFO @ Sun, 21 Jun 2020 19:15:41: Done! pass1 - making usageList (757 chroms): 2 millis pass2 - checking and writing primary data (4561 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:15:44: 17000000 INFO @ Sun, 21 Jun 2020 19:15:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:48: #1 total tags in treatment: 17571004 INFO @ Sun, 21 Jun 2020 19:15:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:15:48: #1 tags after filtering in treatment: 17571004 INFO @ Sun, 21 Jun 2020 19:15:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:49: #2 number of paired peaks: 419 WARNING @ Sun, 21 Jun 2020 19:15:49: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:50: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 19:15:50: #2 alternative fragment length(s) may be 4,100,117 bps INFO @ Sun, 21 Jun 2020 19:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.20_model.r WARNING @ Sun, 21 Jun 2020 19:15:50: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:50: #2 You may need to consider one of the other alternative d(s): 4,100,117 WARNING @ Sun, 21 Jun 2020 19:15:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:15:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:16:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.10_summits.bed INFO @ Sun, 21 Jun 2020 19:16:20: Done! pass1 - making usageList (529 chroms): 2 millis pass2 - checking and writing primary data (1955 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287688/SRX287688.20_summits.bed INFO @ Sun, 21 Jun 2020 19:16:49: Done! pass1 - making usageList (226 chroms): 1 millis pass2 - checking and writing primary data (648 records, 4 fields): 9 millis CompletedMACS2peakCalling